The wilt caused by Fusarium oxysporum f.sp. vasinfectum in cotton is one of the main diseases of this crop. The pathogen is difficult to control because it produces chlamydospores, which allows it to survive in the soil for long periods without the presence of its main host. The control of this disease is based on varieties with some resistance, certified seeds, and fungicides used to treat seeds. Thus, the development of control alternatives is needed to increase the number of resources to manage this disease in the field. Bacillus are bioregulators and antagonists of several important phytopathogens. Therefore, the objective of this work was to select strains of Bacillus (Paenibacillus alvei, Bacillus thuringiensis, B. megaterium, and B. lentus), whose metabolites are toxic to F. oxysporum in laboratory and greenhouse conditions, in addition to adjusting in vitro methodologies to perform and evaluate selection tests. This work determined the best culture medium for the direct confrontation assays, proposed a grading scale to facilitate decisions about selection with the dual tests, identified among the strains selected in the confrontation assays those that produce volatile and non-volatile metabolites toxic to F. oxysporum, and tested these selected strains for disease control during seed germination in greenhouse trials. In last test, some strains of Bacillus had a potential protective effect during the germination of cotton seeds.